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Abstract A novel affinity paper-based electrochemical impedance device (PEID) was first fully developed for cardiovascular risk assessment. Herein, a simple folding PEID comprising a dual screen-printed electrode was fabricated for label-free electrochemical impedance detection. The results demonstrated in a step-wise manner that the phosphocholine-modified screen-printed carbon electrodes were highly responsive to the clinically required range of C-reactive protein (CRP) (0.005 – 500 mg L−1; r2 = 0.993) levels with a detection limit (3σ/slope) of 0.001 mg L−1. The optimal binding frequency of CRP–phosphocholine interaction was determined to be 100 Hz. These results implied that our proposed system could be used for simultaneously measuring the CRP levels using a single PEID platform in combination with the specific recognition elements. When assaying two levels of CRP, the overall assay reproducibility for each concentration, expressed as relative standard error of the mean (RSE%; n = 30), was 1.21%. The variation in the measurements between individual electrodes, expressed as the relative standard deviation (RSD), was 2.82%. Using 2 measurement sites per device, the proposed sensor provided excellent precision for the simultaneous detection of CRP. Moreover, the RSD for the CRP levels measured on ten independently fabricated paper-based sheets was 2.11%, thereby offering an acceptable fabrication reproducibility. The presented folding PEIDs were used forthe determination of CRP in patient-derived blood samples with minimised bias and excellent correlation with a standard method (n = 15; CUSUM linearity test, p > 0.10), thus permitting the potential application of PEID for assessing cardiovascular risk in individuals. Highlights • A PEID was developed for ultrasensitive label-free EIS detection of hs-CRP. • A simply folding step intended to create a small chamber for electrochemical assay. • A single specific-frequency determination facilitates fast impedance measurements. • An excellent agreement was demonstrated between the PEID and the standard method. [ABSTRACT FROM AUTHOR]

In this work, we developed a microfluidic paper-based analytical device (μPAD) for the on-line isolation of proteins and the electrochemical detection of lead ions (Pb(II)) in urine samples. The patterned filter paper was prepared through the direct printing of microchannel patterns on filter paper using an office laser printer. The paper was modified with protein precipitant and was then coupled with a detachable three-electrode system. Experimental parameters, namely, modification reagents, microchannel length and width, deposition potential, and deposition time, were optimized. Then, the maximum protein concentration under which the device can function was obtained as 300 mg L−1. The linear range was 10–500 μg L−1 with a detection limit of 9 μg L−1. The effectiveness of this device was demonstrated through the quantification of Pb(II) in urine samples and the results agreed with those of atomic absorption spectrometry (AAS). • A simple electrochemical paper-based microfluidic device was built using laser printer and 3D printer. • The device enables on-line isolation of proteins in urine. • The maximum protein concentration under which the proposed device can function was 300 mg L−1. • Direct electrochemical detection of Pb in urine was achieved with a detection limit of 9 μg L−1. [ABSTRACT FROM AUTHOR]

Peptide/protein quantitation using mass spectrometry (MS) is advantageous due to its high sensitivity. Traditional absolute peptide quantitation methods rely on making calibration curves using peptide standards or isotope-labelled peptide standards, which are expensive and take time to synthesize. A method which can eliminate the need for using standards would be beneficial. Recently, we developed coulometric mass spectrometry (CMS) which can be used to quantify peptides that are oxidizable (e.g., those containing tyrosine or tryptophan), without using peptide standard. The method is based on electrochemical oxidation of peptides followed by MS measurement of the oxidation yield. However, it cannot be directly used to quantify peptides without oxidizable residues. To extend this method for quantifying peptides/proteins in general, in this study, we adopted a derivatization strategy, in which a target peptide is first tagged with an electroactive reagent such as monocarboxymethylene blue NHS ester (MCMB-NHS ester), followed with quantitation by CMS. To illustrate the power of this method, we have analyzed peptides MG and RPPGFSPFR. The quantification error was less than 5%. Using RPPGFSPFR as an example, the quantitation sensitivity of the technique was found to be 0.25 pmol. Furthermore, we also used the strategy to quantify proteins cytochrome C and β-casein with an error of 2–26 %. [Display omitted] • Coulometric mass spectrometry (CMS) in combination with derivatization strategy can be used for absolute quantitation of peptides and proteins in general. • Our quantitation method reported in this paper does not require the use of standards or isotope-labelled standards. • Our quantitation method reported in this paper is applicable to peptides that are not electrochemically active. • The derivatization of peptide with methylene blue electrochemical tag allows the oxidation of peptides at a very low potential (0.2 V vs. Ag/AgCl), thus providing the method selectivity. [ABSTRACT FROM AUTHOR]

Discovering and accurately locating drug targets is of great significance for the research and development of new drugs. As a different approach to traditional drug development, the machine learning algorithm is used to predict the drug target by mining the data. Because of its advantages of short time and low cost, it has received more and more attention in recent years. In this paper, we propose a novel method for predicting druggable proteins. Firstly, the features of the protein sequence are extracted by combining Chou's pseudo amino acid composition (PseAAC), dipeptide composition (DPC) and reduced sequence (RS), getting the 591 dimension of drug target dataset. Then, the feature information of druggable proteins dataset is selected by genetic algorithm (GA). Finally, we use Bagging ensemble learning to improve SVM classifier to get the final prediction model. The predictive accuracy rate reaches 93.78% by using 5-fold cross-validation and compared with other state-of-the-art predictive methods. The results indicate that the method proposed in this paper has a high reference value for the prediction of potential drug targets, which will successfully play a key role in the drug research and development. The source code and all datasets are available at https://github.com/QUST-AIBBDRC/GA-Bagging-SVM. [ABSTRACT FROM AUTHOR]

During Herbert Tabor's tenure as Editor-in-Chief from 1971 to 2010, JBC has published many seminal papers in the fields of chromatin structure, epigenetics, and regulation of transcription in eukaryotes. As of this writing, more than 21,000 studies on gene transcription at the molecular level have been published in JBC since 1971. This brief review will attempt to highlight some of these ground-breaking discoveries and show how early studies published in JBC have influenced current research. Papers published in the Journal have reported the initial discovery of multiple forms of RNA polymerase in eukaryotes, identification and purification of essential components of the transcription machinery, and identification and mechanistic characterization of various transcriptional activators and repressors and include studies on chromatin structure and posttranslational modifications of the histone proteins. The large body of literature published in the Journal has inspired current research on how chromatin organization and epigenetics impact regulation of gene expression. [ABSTRACT FROM AUTHOR]

Commitment to apoptotic cell death occurs at the mitochondria and is regulated by BCL-2 family proteins localized to this organelle. However, BIK, a resident protein of the endoplasmic reticulum, inhibits mitochondrial BCL-2 proteins to promote apoptosis. In a recent paper in the JBC, Osterlund et al. investigated this conundrum. Surprisingly, they discovered that these endoplasmic reticulum and mitochondrial proteins moved toward each other and met at the contact site between the two organelles, thereby forming a 'bridge to death'. [ABSTRACT FROM AUTHOR]

When yeast cells enter into quiescence in response to nutrient limitation, the adenine deaminase Aah1p is specifically degraded via a process requiring the F-box protein Saf1p and components of the Skp1-Cullin-F-box complex. In this paper, we show that Saf1p interacts with both Aah1p and Skp1p. Interaction with Skp1p, but not with Aah1p, requires the F-box domain of Saf1p. Based on deletion and point mutations, we further demonstrate that the F-box domain of Saf1p is critical for degradation of Aah1p. We also establish that overexpression of Saf1p in proliferating cells is sufficient to trigger the degradation of Aah1p. Using this property and a two-dimensional protein gel approach, we found that Saf1p has a small number of direct targets. Finally, we isolated and characterized several point mutations in Aah1p, which increase its stability during quiescence. The majority of the mutated residues are located in two distinct exposed regions in the Aah1p three-dimensional model structure. Two hybrid experiments strongly suggest that these domains are directly involved in interaction with Saf1p. Importantly, we obtained a mutation in Aah1p that does not affect the protein interaction with Saf1p but abolishes Aah1p degradation. Because this mutated residue is an exposed lysine in the Aah1p three-dimensional model, we propose that it is likely to be a major ubiquitylation site. All together, our data strongly argue for Saf1p being a bona fide Skp1-Cullin-F-box subunit. [ABSTRACT FROM AUTHOR]

The influence of different wastewater compositions on the extracellular polymer substances (EPS) (protein, polysaccharide and DNA) and physicochemical properties (surface charge, bound water and contact angle) were studied in continuous fed completely stirred tank reactor (CSTR). Five laboratory-scale activated sludge reactors were operated under steady-state conditions. Protein was the predominant polymer followed by polysaccharide and DNA. Lower amounts of protein and higher DNA levels were found in the extracellular substances from flocs grown on more complex organics and substrates. A high level of protein (nearly 70 mg g−1 VSS) and a low DNA content (nearly 6 mg g−1 VSS) were measured in the EPS of the winery industry and municipal activated sludge while lower levels of protein (approximately 38–42 mg g−1 VSS) and higher levels of DNA content (approximately 11–17 mg g−1 VSS) were measured in the pulp-paper, textile (cotton knit fabrics) and petrochemical floc EPSs under steady-state conditions. Flocs with small (36 μm) and large (nearly 130 μm) diameters were observed in the pulp-paper, textile and petrochemical industries, respectively, associating with high SVI values. Larger contact angles (between 37 and 42°), low negatively charged surface values (between −0.11 and −0.25 meq g−1 VSS) and high amounts of bound water (between 20 and 24 g g−1 TSS) were determined in the pulp-paper, textile and petrochemical industry activated sludge samples. However, floc samples from the municipal and winery industry activated sludge had small contact angles (between 7 and 9°) and low bound water content (7–9 g g−1 TSS) together with high surface charge values (between −0.55 and −0.61 meq g−1 VSS), indicating good settleability. Since the reactor design of the five laboratory-scale reactor were similar and different wastewater were compared, it can be said that the EPS composition depends more on wastewater type rather than operating conditions. [Copyright &y& Elsevier]

Prediction of protein structural class plays an important role in protein structure and function analysis, drug design and many other biological applications. Prediction of protein structural class for low-similarity sequences is still a challenging task. Based on the theory of wavelet denoising, this paper presents a novel method of prediction of protein structural class for the first time. Firstly, the features of the protein sequence are extracted by using Chou’s pseudo amino acid composition (PseAAC). Then the extracted feature information is denoised by two-dimensional (2D) wavelet. Finally, the optimal feature vectors are input to support vector machine (SVM) classifier to predict protein structural classes. We obtained significant predictive results using jackknife test on three low-similarity protein structural class datasets 25PDB, 1189 and 640, and compared our method with previous methods The results indicate that the method proposed in this paper can effectively improve the prediction accuracy of protein structural class, which will be a reliable tool for prediction of protein structural class, especially for low-similarity sequences. [ABSTRACT FROM AUTHOR]

• A new benchmark of protein surfaces equipped with three physicochemical properties. • Protein surfaces are retrieved and classified with respect to different ground truths. • Analysis of the retrieval and classification performances of the methods that participated in SHREC 2021. • A thorough Investigation of how different physicochemical properties impact the performance of retrieval methods. [Display omitted] This paper presents the methods that have participated in the SHREC 2021 contest on retrieval and classification of protein surfaces on the basis of their geometry and physicochemical properties. The goal of the contest is to assess the capability of different computational approaches to identify different conformations of the same protein, or the presence of common sub-parts, starting from a set of molecular surfaces. We addressed two problems: defining the similarity solely based on the surface geometry or with the inclusion of physicochemical information, such as electrostatic potential, amino acid hydrophobicity, and the presence of hydrogen bond donors and acceptors. Retrieval and classification performances, with respect to the single protein or the existence of common sub-sequences, are analysed according to a number of information retrieval indicators. [ABSTRACT FROM AUTHOR]

This paper presents a comprehensive analysis of deep transfer learning methods, supervised methods, and semi-supervised methods in the context of protein fitness prediction, with a focus on small datasets. The analysis includes the exploration of the combination of different data sources to enhance the performance of the models. While deep learning and deep transfer learning methods have shown remarkable performance in situations with abundant data, this study aims to address the more realistic scenario faced by wet lab researchers, where labeled data is often limited. The novelty of this work lies in its examination of deep transfer learning in the context of small datasets and its consideration of semi-supervised methods and multi-view strategies. While previous research has extensively explored deep transfer learning in large dataset scenarios, little attention has been given to its efficacy in small dataset settings or its comparison with semi-supervised approaches. Our findings suggest that deep transfer learning, exemplified by ProteinBERT, shows promising performance in this context compared to the rest of the methods across various evaluation metrics, not only in small dataset contexts but also in large dataset scenarios. This highlights the robustness and versatility of deep transfer learning in protein fitness prediction tasks, even with limited labeled data. The results of this study shed light on the potential of deep transfer learning as a state-of-the-art approach in the field of protein fitness prediction. By leveraging pre-trained models and fine-tuning them on small datasets, researchers can achieve competitive performance surpassing traditional supervised and semi-supervised methods. These findings provide valuable insights for wet lab researchers who face the challenge of limited labeled data, enabling them to make informed decisions when selecting the most effective methodology for their specific protein fitness prediction tasks. Additionally, the study investigated the combination of two different sources of information (encodings) through our enhanced semi-supervised methods, yielding noteworthy results improving their base model and providing valuable insights for further research. The presented analysis contributes to a better understanding of the capabilities and limitations of different learning approaches in small dataset scenarios, ultimately aiding in the development of improved protein fitness prediction methods. • Deep transfer learning excels in small dataset protein fitness prediction. • We explore labeled-unlabeled data combination through semi-supervised learning. • We developed enhanced semi-supervised methods for regression and multi-view tasks. • Information combination from different encodings holds potential for future research. • Insights can aid wet lab researchers in selecting protein fitness prediction methods. [ABSTRACT FROM AUTHOR]

Chronic diseases are becoming more prevalent, and the complexities of managing patients continue to escalate, since their care must be balanced between the home and clinical settings. Diabetes is the most advanced example, where self-monitoring has been shown to be necessary. Glucometers are point-of-care (POC) devices that have become standard platforms at home and clinical settings. Similarly, many other POC biosensors have also been developed. Enzymes are often used in these sensors because of their specificity and the reaction products can be electrochemically transduced for the measurement. When enzymes are immobilized to an electronically active substrate, enzymatic reactions can be transduced by direct electron transport. This paper describes an approach for the development of graphene-based POC devices. This includes modifying enzymes for improved performance, developing methods to bind them to the graphene surface, incorporation of the functionalized graphene on a field-effect transistor (FET), and integration into a microfluidic device suitable for home use. This paper describes an approach for the development of a graphene-based POC biosensor platform using glucose as an example of target molecule. [ABSTRACT FROM AUTHOR]

A protein coat, termed the protein corona, assembles around the nanocarriers´ surface once it gets in contact with a biological environment. We show that the media used for the washing of protein corona can be crucial. This is true for the downstream analysis as well as for the pre-coating used in in vitro or in vivo. This has been widely overlooked so far. In this paper we focus on eight different washing media and analyze how they influence the composition of the hard protein corona of several nanocarriers incubated with human blood plasma and serum. SDS-PAGE and LC-MS analysis showed major differences in protein corona profiles when using diverse washing media. While plasma and serum proteins already have different complexities, each washing media changes the composition of proteins detected by downstream methods with different key proteins bound to the nanocarriers´ surface. Furthermore, the protein structure of the most abundant blood proteins incubated in the different media was analyzed with nanoDSF. This also emphasized the importance of the washing media, which had a significant influence on the protein adsorption stability. Lastly, cell uptake experiments for HeLa and RAW 264.7 macrophages also indicated an influence of the washing media. In conclusion, picking a specific washing media is on the one hand an important factor for downstream detection of protein compositions and may on the other hand be used to deliberately tune the protein corona for pre-adsorbed proteins from complex protein compositions. This might further support a guided delivery of the nanocarrier to a desired location within a physiological environment. The successfully application of nanocarriers as drug delivery vehicles is currently hampered by a limited understanding of the nanocarriers´ behavior in a complex biological environment. Once the nanocarrier comes into contact with blood plasma or serum, biomolecules rapidly adsorb onto their surface, covering the nanocarriers and forming a protein corona, which then dictates their biological identity. Analyzing the composition of this dynamic network of bound molecules, has already been shown to be influenced by various factors. However, the impact of the washing media used for the protein corona preparation has so far been neglected. In the present study, we demonstrate a quantitative influence of the washing media on the composition of the hard corona of different nanocarrier systems, which additionally affects protein stability and cellular uptake behavior. Image, graphical abstract [ABSTRACT FROM AUTHOR]

Amyloid fibers formed by the aggregation of amyloid proteins can lead to various neurological diseases. Accurate prediction of amyloid proteins can provide scientific basis for exploring the pathogenesis of related neurological diseases, and developing targeted treatment plans. In view of the limitations of the synthetic minority over-sampling technique (SMOTE), an improved SMOTE method based on density clustering is proposed in this paper, and combined with multi-view features to construct an amyloid protein prediction model. The benefits of this enhanced SMOTE method include eliminating problematic samples, accomplishing an evenly distributed minority sample pool, and utilizing all available boundary sample information. Compared with other over-sampling methods, this method can effectively improve the authenticity and representativeness of the synthesized samples, and has a strong ability to process imbalanced data. After the dataset is over-sampling, different prediction algorithms are trained respectively to construct the baseline models. To fully characterize proteins, the probability and category features are extracted from the baseline models and combined with the sequence features selected by CFS-GSSS (Correlation-based Feature Selection Combined with Greedy Stepwise Search Strategy) to generate the multi-view features. Experimental results demonstrate the complementarity and feasibility of the multi-view features. On the independent test set, compared with the existing best model (ECAmyloid), the proposed amyloid protein prediction model improved the sensitivity and geometric mean by 0.0706 and 0.0129, respectively, far superior to other existing methods. • Sequence composition, evolutionary, structural and physicochemical properties are extracted. • Correlation-based Feature Selection is performed to remove redundancy features. • A density-based minority over-sampling technique is proposed to balance the dataset. • Multi-view features are proposed to fully characterize the proteins. • Compared with existing methods, the proposed predictor exhibits superior performance. [ABSTRACT FROM AUTHOR]

The article presents abstracts of papers published within the issue, including one on the use of mid-infrared spectroscopy (MIRS) in predicting new milk phenotypes, another on mouth drying caused by dairy proteins and a paper on the effect of feeding canola meal on concentrations of plasma amino acids.

Abstract: High throughput process development (HTPD) platforms provide time and resource effective solutions for optimization of resin as well as membrane based chromatography processes. They enable successful implementation of Quality by Design by allowing us to investigate more variables and wider ranges than would be possible using traditional lab-scale based experiments. This paper presents an investigation about non-specific protein adsorption that was found to occur on the membrane disks used in a commercially available high throughput device. Both qualitative as well as quantitative analytical tools were used in this investigation. Two biotherapeutic protein molecules, granulocyte colony stimulating factor (GCSF) and Transtuzumab were selected as model proteins in this study. Qualitative assessment was performed using Attenuated Total Reflectance Fourier-Transform Infrared Spectroscopy (ATR-FTIR), Scanning Electron Microscopy (SEM) and Atomic Force Microscopy (AFM). An empirical model based on contact angle measurement was developed for quantitative assessment of the amount of adsorbed protein. The results indicated that while significant non-specific adsorption was observed in case of highly hydrophobic GCSF molecule, adsorption was minimal in the case of Transtuzumab. The paper proposes a novel use of contact angle measurement for quantitative estimation of adsorbed protein. The study also highlights the importance of accounting for non-specific adsorption when using these HTPD devices. [Copyright &y& Elsevier]

Abstract: Computational annotation of protein functions and structures from sequence features, or prediction of certain diseases from gene expression levels are among important applications of computational biology. Developing methods capable of such predictions are not only important in terms of their biological and medical uses but also a very challenging task of pattern recognition due to high input dimensionality and small sample size. Ensemble and multi-view learning has gained popularity due to the rapid rise of such datasets (such as the protein and arrhythmia datasets used in this paper) with large numbers of variables. However, the classical ensemble approach does not take into account conditional interdependences among the views. In this paper, we present a two stage supervised multi-view learning technique called parallel interacting multi-view learning (PIML). In the first stage of PIML, similar to the ensemble method, the views are individually used by a predictor, and the class posterior probability estimates are obtained. In the second stage, each view is trained using its own features along with the class posterior probability estimates of the other views as the summary information of other views. This is a hybrid way of combining the views in which the views influence each other during training using the predictions of others interdependences. PIML is demonstrated and compared with the classical ensemble approach on three real datasets. [Copyright &y& Elsevier]

• The review discussed advantages of US for plant protein industrial applications. • Traditional plant protein extraction techniques exhibit key industrial bottlenecks. • US can enhance plant protein yield and functionality by disrupting structural cells. • The plant protein industry requires advanced US to maximize profit/greener impacts. The present-day consumer is not only conscious of the relationship between food consumption and positive health, but also keen on environmental sustainability. Thus, the demand for plant-based proteins, which are associated with nutrition and environmental sustainability. However, the plant-based protein industry still demands urgent innovation due to the low yield and long extraction time linked with traditional extraction methods. Although ultrasound is an eco-innovative technique, there exist limited data regarding its impact with plant-based protein. In this paper, the scientific principles of ultrasonication with regards to its application in plant-based protein research were reviewed. After comparing the cavitational and shearing impacts of different ultrasonic parameters, the paper further reviewed its effects on extracted protein characteristics and techno-functional properties. Additionally, current technological challenges and future perspectives of ultrasonication for the plant-based protein industry were also discussed. In summary, this review does not only present the novelty and environmental sustainability of ultrasound as a plant-based protein assisted-extraction method, but also highlights on the correlation between protein source, structure and subsequent functional properties which are important crucial factors for maximum application of ultrasound in the growing plant-based protein market. [ABSTRACT FROM AUTHOR]

Abstract: This paper provides an overview of different nanostructured architectures utilised in electrochemical devices and their application in biosensing and bioelectronics. Emphasis is placed on the fabrication of nanostructured films based on a layer-by-layer (LBL) films approach. We discuss the theory and the mechanism of charge transfer in polyelectrolyte multilayer films (PEM), as well as between biomolecules and redox centres, for the development of more sensitive and selective biosensors. Further, this paper presents an overview of topics involving the interaction between nanostructured materials, including metallic nanoparticles and carbon materials, and their effects on the preservation of the activity of biological molecules immobilised on electrode surfaces. This paper also presents examples of biological molecules utilised in film fabrication, such as DNA, several kinds of proteins, and oligonucleotides, and of the role of molecular interaction in biosensing performance. Towards the utilisation of LBL films, examples of several architectures and different electrochemical approaches demonstrate the potential of nanostructured LBL films for several applications that include the diagnosis and monitoring of diseases. Our main aim in this review is to survey what can assist researchers by presenting various approaches currently used in the field of bioelectrochemistry utilising supramolecular architectures based on an LBL approach for application in electrochemical biosensing. [Copyright &y& Elsevier]

Blunt force trauma is the most common injury found during autopsies. Among the cases involving blunt force injuries, fractures to the skull are the most frequent, and these are often fatal to the victim. Understanding the circumstances surrounding the creation of such injuries is essential for investigating trauma-related deaths. This paper explores the characteristics of cranial trauma produced following one to three consecutive blows with a series of blunt objects. Fourteen Synbone® spheres filled with porcine gelatine and coated with rubber skin were used to simulate the human skull in a series of experiments. Trials recreated two scenarios, individuals standing and individuals with their head resting against a hard surface. Six blunt objects were used to represent possible weapons. Each sphere was struck twice to generate fracture patterns, which were then analysed. In most simulations of a blow to the head resting against a hard surface, the first fracture follows a linear pattern regardless of the direction of force and/or the surface of the weapon; while the second blow results in a depressed fracture. In the case of a free moving head, weapons with large contact surfaces result in depressed fractures, while weapons with small contact surfaces may not cause a fracture at all. Our results are consistent with Moritz who stated that, if the head is free to move, the fractures will be linear or incompletely depressed. Inversely, if the head rests against a solid surface, a blow will result in a depressed fracture. More experiments are needed to verify these preliminary observations. [ABSTRACT FROM AUTHOR]

The adsorption of proteins is the initiating event in the processes occurring when blood contacts a "foreign" surface in a medical device, leading inevitably to thrombus formation. Knowledge of protein adsorption in this context has accumulated over many years but remains fragmentary and incomplete. Moreover, the significance and relevance of the information for blood compatibility are not entirely agreed upon in the biomaterials research community. In this review, protein adsorption from blood is discussed under the headings "agreed upon" and "not agreed upon or not known" with respect to: protein layer composition, effects on coagulation and complement activation, effects on platelet adhesion and activation, protein conformational change and denaturation, prevention of nonspecific protein adsorption, and controlling/tailoring the protein layer composition. This paper is part 2 of a series of 4 reviews discussing the problem of biomaterial associated thrombogenicity. The objective was to highlight features of broad agreement and provide commentary on those aspects of the problem that were subject to dispute. We hope that future investigators will update these reviews as new scholarship resolves the uncertainties of today. [ABSTRACT FROM AUTHOR]

In this paper, we report on an integrated nanorod array as a novel sieving matrix for high-resolution separation of biomolecules. A wide size range of DNA (100 bp–166 kbp) and proteins (11.4 kDa–205 kDa) are resolved into sharp peaks within several minutes using devices with various pore apertures, either in a reptation mode or Ogston mechanism. The device delivers notable performance with the minimum resolvable size difference 10 bp for 100 bp and 150 bp DNA fragments, 15.9 kbp for 48 kbp and 166 kbp DNA chains, and 7.9 kDa for 11.4 and 68 kDa proteins, where the separation efficiency is higher than or comparable to other micro/nanofabricated artificial sieving structures. The process utilizes localized oblique angle deposition (LOAD) to simply integrate densely packed nanorods onto steep sidewalls of microfluidic channels, which eliminates the requirement of advanced lithography tools routinely used in conventional artificial sieving structures. We further demonstrate the modulation of pore aperture that employs the sculptured sidewalls by a custom deep reactive-ion etching (DRIE) recipe. Given the easy fabrication, excellent engineering control and outstanding sieving capability, this nanorod sieve device has great potentials to provide a simple and effective separation technique for biomolecule analysis. • A unique sieving matrix consisting of nanorod arrays was demonstrated for gel-free fractionation of DNA and proteins. • A wide size range of DNA (100 bp–166 kbp) and proteins (11.4 kDa–205 kDa) were resolved within several minutes. • A simple physical vapor deposition was utilized to easily integrate three dimensional oxide nanorods into separation device. [ABSTRACT FROM AUTHOR]

The current allergenicity assessment of novel proteins is based on the EFSA GMO guidance. Recently, EFSA launched a new guidance document on allergenicity assessment of GM plants (2017). This document describes, amongst other topics, the new scientific and regulatory developments on in vitro protein digestibility tests. The EFSA GMO Panel stated that for in vitro protein digestibility tests, additional investigations are needed before any additional recommendation in the form of guidance can be provided. To this end, an interim phase is considered necessary to evaluate the revisions to the in vitro gastrointestinal digestion test, proposed by EFSA. This prompted the establishment of a joint workshop through two COST Action networks: COST Action ImpARAS and COST Acton INFOGEST. In 2017, a workshop was organised to discuss the relevance of digestion in allergenicity risk assessment and how to potentially improve the current methods and readouts. The outcome of the workshop is that there is no rationale for a clear readout that is predictive for allergenicity and we suggest to omit the digestion test from the allergenicity assessment strategy for now, and put an effort into filling the knowledge gaps as summarized in this paper first. • Protein digestion is relevant for allergenicity of some proteins, but not for all. • It is not clear yet how different factors exactly influence digestion and how these factors can be included. • Including all factors will complicate the elaboration of a simple and predictive digestion assay. • There is no rationale for a clear readout that is predictive for allergenicity. • We suggest to omit the digestion test from the allergenicity assessment for now and put effort into filling the knowledge gaps. [ABSTRACT FROM AUTHOR]

Cellular processes are typically carried out by protein complexes rather than individual proteins. Identifying protein complexes is one of the keys to understanding principles of cellular organization and function. Also, protein complexes are a group of interacting genes underlying similar diseases, which points out the therapeutic importance of protein complexes. With the development of life science and computing science, an increasing amount of protein-protein interaction (PPI) data becomes available, which makes it possible to predict protein complexes from PPI networks. However, most PPI data produced by high-throughput experiments often has many false positive interactions and false negative edge loss, which makes it difficult to predict complexes accurately. In this paper, we present a new method, named as MEMO (Multiple network Embedding for coMplex detectiOn), to detect protein complexes. MEMO integrates multiple PPI datasets from different species into a single PPI network by using functional orthology information across multiple species and then uses a graph embedding technology to embed protein nodes of the network into continuous vector spaces, so as to quantify the relationships between nodes and better guild the protein complex detection process. Finally, it utilizes a seed-and-extend strategy to identify protein complexes from multiple PPI networks based on the similarities of their corresponding protein representations. As part of our approach, we also define a new quality measure which combines the cluster cohesiveness and cluster density to measure the likelihood of a detected protein complex being a real protein complex. Extensive experimental results demonstrate the proposed method outperforms state-of-the-art complex detection techniques. [ABSTRACT FROM AUTHOR]

Many food innovations rely on the introduction and use of new or modified proteins. New or modified food proteins may lead to major health risks due to their inherent potential to cause food allergy. Currently, the pre-market allergenicity assessment for new or modified food proteins and protein sources relies on methods for identifying allergenic hazards based on characteristics of known allergens. However, there is no general consensus on the allergenicity parameters to use and the criteria that should apply for the evaluation and decisions to be made. In this paper, we propose that the strategy for allergenicity risk assessment of new or modified food proteins and the methodologies applied should be governed by the risk management questions to be answered, reflected in the information needed by risk managers to enable their informed decision making. We generated an inventory of health outcome-related assessment parameters and criteria potentially important for risk management decision-making and we discuss the implications of selecting different optional criteria (e.g. cut-off values) for what could be accepted as safe with regards to the health outcomes in the (at risk) population. The impact of these various options on both method development and risk management practices was investigated. • New or modified food proteins may lead to food allergy and require risk assessment. • There is no guidance on allergenicity parameters and evaluation criteria to use. • Allergenicity risk assessment should be governed by the risk management questions. • Methodologies should be governed by the information needed by the risk manager. • We present an inventory of optional assessment parameters and evaluation criteria. [ABSTRACT FROM AUTHOR]

Abstract Marine resources are limited and optimal utilisation of all the available material is essential to ensure sustainability. This brings two main challenges: the first is to get the maximum quantity and quality out of the catch of high value-added raw material. The second is to upgrade low value-added raw material such as blood-waters. The volume of blood-waters generated from pelagic processing industries and their organic load varies from species to species but volumes are large and costs associated with disposal are substantial. However, pelagic blood-water waste streams contain proteins, lipids and small molecules with potential for use in food and feed. The dog and cat feed and food industry is a lucrative sector which is currently valued at $42 billion and is considerably larger than the worldwide baby food market. Furthermore, blood-water from processing is a substantial environmental and economic cost for pelagic processors. To date, the utilisation of blood-waters as food and feed ingredients has not been intensively reviewed. The central focus of this paper is to provide a comprehensive and critical review of recent progress in the recovery of proteins and other molecules from pelagic fish derived blood-waters using filtration and other methods which have potential for use by food and feed industries. The current and potential applications of blood-waters are discussed and the review confirms that blood-water recovery technologies are viable and environmentally beneficial but production efficiency and costs should be improved. The review also provides analysis of challenges that exist concerning the development of ingredients from this resource including the relevant legislation and regulation governing access/use of blood-water and limitations that can be encountered in the development of products. Recent research indicates that proteins derived from blood-waters which are obtained in properly managed processing plants can be considered safe if handled correctly and have potential to replace proteins from other sources in fish and feed manufacture. It is recommended that the safety of recovered pelagic blood-waters in terms of the microbial and heavy metal load is assessed prior to use and that further research should be carried out in conjunction with industry to reduce costs associated with implementation of successful filtration methods. This review provides scientific value for marine and food scientists concerning recovery and utilisation strategies of pelagic processing blood-waters and this may be used to inform industry and environmental policy makers in the future. Graphical abstract Image 1 Highlights • Review collates the current state-of-the-art concerning treatment of blood-water prior to release at sea. • Details potential markets and challenges associated with these markets for proteins recovered from bloodwaters. • Details potential health and technofunctional properties of recovered blood-water proteins. [ABSTRACT FROM AUTHOR]

Abstract This paper primarily demonstrates the approach to enhance the sensing performance on antigen C-reactive protein (CRP) and anti-CRP antibody binding event. A nanogapped electrode structure with the gap of ~100 nm was modified by the anti-CRP antibody (Probe) to capture the available CRP. In order to increase the amount of antigen to be captured, a gold nanorod with 119 nm in length and 25 nm in width was integrated, to increase the surface area. A comparative study between the existence and non-existence of gold nanorod utilization was evaluated. Analysis of the sensing surface was well-supported by atomic force microscopy, scanning electron microscopy, 3D nano-profilometry, high-power microscopy and UV–Vis spectroscopy. The dielectric voltammetric analysis was carried out from 0 V to 2 V. The sensitivity was calculated based on 3σ and attained as low as 1 pM, which is tremendously low compared to real CRP concentration (119 nM) in human blood serum. The gold nanorod conjugation with antibody has enhanced the sensitivity to 100 folds (10 fM). The specificity of the CRP detection by the proposed strategy was anchored by ELISA and failure in the detection of human blood clotting factor IX by voltammetry. Despite, CRP antigen was further detected in human serum by spiking CRP to run-through the detection with the physiologically relevant samples. Highlights • Nanogapped sensor modified by anti-C-reactive protein (CRP) antibody to bind CRP. • A gold nanorod with 119 nm in length was integrated, to increase the sensitivity. • Gold nanorod conjugation with antibody has enhanced the sensitivity to 100 folds. • Specificity was anchored by ELISA and with human blood clotting factor IX. • CRP antigen was further detected in human serum by spiking CRP. [ABSTRACT FROM AUTHOR]

Abstract A variety of models and hypothesis have been proposed to interpret the temperature dependence of the mean square displacement (MSD) of protein, that is obtained from the incoherent neutron scattering measurement, but a consensus seems yet to be achieved. The most controversial point is concerned with the physics behind the abrupt change of gradient of MSD plotted against temperature. The phenomenon is attributed to different physics by different authors, such as glass transition, alpha to beta transition, harmonic to anharmonic transition, coupling of protein and hydrated-water dynamics, and so forth. In the present paper, we propose a theory to analyse the elastic incoherent neutron scattering (EINS) data of aqueous solutions of protein, based on the generalized Langevin theory combined with the 3D-RISM/RISM equation [B. Kim and F. Hirata, J. Chem. Phys., 138, 054108 (2012)]. The theory gives closed equations for the elastic incoherent structure factor (EISF) and MSD as a function of temperature. Based on the theory, the abrupt change of the gradient of MSD in the temperature dependence is interpreted as an onset of " solvent - induced elasticity ," or "free energy elasticity," with increasing temperature. Highlights • A theory to analyse the incoherent neutron scattering data of protein is proposed. • The equation is derived based on the generalized Langevin theory and 3D-RISM. • The theory gives a closed equation for MSD as a function of temperature. • The inflection temperature of MSD is interpreted by solvent - induced elasticity. [ABSTRACT FROM AUTHOR]

Abstract: This paper investigates the effect of degradation of proteins transported by means of slow axonal transport (due to enzyme-mediated breakdown of proteins) on the speed of the bell-shaped wave of protein concentration propagating toward the synapse of the axon. Another issue investigated in this paper is the effect of protein degradation on the traffic jam caused by a decay of microtubule tracks at a certain location in the axon. The decay of microtubule tracks may be caused by misregulation of microtubule-associated proteins resulting from an imbalance in intracellular signaling or by mutations of these proteins. Axonal swellings caused by such traffic jams hinder axonal transport; they are a likely cause of various neurodegenerative diseases, including Alzheimer''s and Parkinson''s diseases and the Down syndrome. [Copyright &y& Elsevier]

Abstract: The study was aimed to estimate whether rat''s exposure to cadmium (Cd; 50mg/l in drinking water for 12 weeks) and/or ethanol (EtOH; 5g/kg b.wt./24h p.o. for 12 weeks), noted by us to induce oxidative stress and stimulate lipid peroxidation, can cause oxidative damage to proteins and DNA, and whether and to what extent the effects of co-exposure differ from those observed under the treatment with each substance alone. Protein carbonyl groups (PC) and protein thiol groups (PSH) in the serum, liver and kidney, as markers of oxidative protein damage, and 8-hydroxy-2′-deoxyguanosine (8-OHdG) in the serum, as a marker of DNA oxidation, were determined. The exposure to Cd or/and EtOH led to oxidative protein damage (increased PC and decreased PSH concentrations in the serum and/or liver), and to DNA oxidation (increased 8-OHdG concentration in the serum). The effects were more advanced at the co-exposure than at the treatment with each substance alone. The more serious damage to proteins and DNA at the co-exposure to Cd and EtOH seems to be the effect of independent action of both xenobiotics. The results of the present paper together with our recent findings in the same rats seem to indicate that at co-exposure to Cd and EtOH proteins and DNA may be more vulnerable to oxidation than lipids. The paper is the first report suggesting that excessive EtOH consumption during exposure to Cd may increase the risk of health damage via enhancing protein and DNA oxidation. [Copyright &y& Elsevier]

Abstract: The present paper aims at introducing and discussing to some extent the possibility of endowing the set of all possible protein chains–which, being obviously empirically unknown, will be thought of as a mathematical object, i.e. a sample space –with the structure of a topological space. The main goal of the discussion is to try to identify some kind of (statistical) law linking classes of sequences to distributions of suitably defined local geometric properties of the chains folded in the native configurations of proteins. This should enable one to translate the physical multiple interactions leading to the final configuration of a protein into stochastically defined multiple interactions between individuals whose states are described by geometric parameters only. To achieve our goal, we need a suitable notion of (pseudo-)distance between primary structures, which could improve the one introduced in a previous paper, and allow us to give a corresponding definition of stability of local geometric structures (and, as a consequence, of three-dimensional configurations) of proteins. [Copyright &y& Elsevier]

Abstract: In chromatography, macromolecules do not adsorb in the traditional sense of the word but bind to ligands that are covalently bonded to the surface of the porous bead. Therefore, the adsorption must be modelled as a process where protein molecules bind to the immobilised ligands. The paper discusses the general thermodynamic principles of ligand binding. Models of the multi-component adsorption in ion-exchange and hydrophobic chromatography, HIC and RPLC, are developed. The parameters in the models have a well-defined physical significance. The models are compared to the Langmuir model. In the traditional adsorption models, the standard state Gibbs energy change of adsorption does not depend level of occupancy, but when it depends on the level of occupancy it gives rise to an adsorptive behaviour known as cooperativity. The binding of oxygen to haemoglobin is a well-known example from biology but it is also observed in chromatography due to protein–protein interactions. Retention measurements on β-lactoglobulin A demonstrate this. A discussion of salt effects on hydrophobic interactions in precipitation and chromatography of proteins concludes the paper. [Copyright &y& Elsevier]

Abstract: Human mitogen-activated protein (MAP) kinase interacting kinase 1b (Mnk1b) is a splice variant of human Mnk1a, which has been identified in our laboratory [A. O’Loghlen, V.M. Gonzalez, D. Pineiro, M.I. Perez-Morgado, M. Salinas, M.E. Martin, Identification and molecular characterization of Mnk1b, a splice variant of human MAP kinase-interacting kinase Mnk1, Exp. Cell Res. 299 (2004) 343–355]. Mnk1b has much higher basal eIF4E kinase activity than Mnk1a. Because Mnk1b presents different features in its C-terminus with respect to Mnk1a, we have studied in this paper the potential role of these structural differences in determining the higher basal eIF4E kinase activity as well as the subcellular localization of Mnk1b. In this paper, we demonstrate that phosphorylation of the Thr209 and Thr214 in the activation loop of Mnk1b is necessary for its activation. However, the different kinase activity between Mnk1a and Mnk1b is independent of the phosphorylation status of the activation loop residues. By deletion of the C-terminal tail in Mnk1a, we confirmed that the absence of this sequence is not responsible for the higher eIF4E kinase activity present in Mnk1b. Moreover, our findings support a crucial role of the 12 amino acids, particularly the Ala344, in the C-terminal specific region of Mnk1b (Mnk1bSR), on the kinase activity of the protein. [Copyright &y& Elsevier]

Abstract: One of the important issues in the synthesis of nanoparticles (NPs) is knowing how to regulate the particle size. The use of a protein cavity (cage) as the growth field of NPs provides one candidate method for obtaining uniform particle size. The present paper reviews several examples of fabricating inorganic NPs using proteins, in particular ferritin and Dps. An additional advantage of using a protein cavity has to do with the specific interactions between proteins. Proteins will crystallize under certain special conditions, yielding regularly arranged sites for NPs. Thus, protein crystallization enables the formation of a regular array of NPs. This paper also reviews the fabrication of two-dimensional NP arrays on a solid surface using ferritin. [Copyright &y& Elsevier]

Abstract: Peptides in solution currently exist under several conformations; an equilibrium which varies with solvent polarity. Despite or because of this structure versatility, peptides can be selective biological tools: they can adapt to a target, vary conformation with solvents and so on. These capacities are crucial for cargo carriers. One promising way of using peptides in biotechnologies is to decipher their medium–sequence–structure–function relationships and one approach is molecular modelling. Only few “in silico” methods of peptide design are described in the literature. Most are used in support of experimental screening of peptide libraries. However, the way they are made does not teach us much for future researches. In this paper, we describe an “in silico” method (PepDesign) which starts by analysing the native interaction of a peptide with a target molecule in order to define which points are important. From there, a modelling protocol for the design of ‘better’ peptides is set. The PepDesign procedure calculates new peptides fulfilling the hypothesis, tests the conformational space of these peptides in interaction with the target by angular dynamics and goes up to the selection of the best peptide based on the analysis of complex structure properties. Experimental biological assays are finally used to test the selected peptides, hence to validate the approach. Applications of PepDesign are wide because the procedure will remain similar irrespective of the target which can be a protein, a drug or a nucleic acid. In this paper, we describe the design of peptides which binds to the fusogenic helical form of the C-terminal domain of the Aβ peptide (Aβ29–42). [Copyright &y& Elsevier]

Abstract: The deinking of MOW is examined at laboratorial scale. The effect of deinking aids, pre-washing and mixing are studied. The operating conditions during pulp treatment affect the pulp and paper properties, interfering with the mechanism of ink removal and modifying the ink particle characteristics. Pre-washing the pulp facilitates the deinking process. Cellulolytic enzymes and deinking chemicals are comparable in terms of ink removal ability. [Copyright &y& Elsevier]

Abstract: To have efficient data mining systems, we need powerful algorithms to extract and mine the data. In the case of genomes data mining system, the algorithms search for genomes/proteins that share similar properties. Proteins that have a significant biological relationship to one another often share only isolated regions of sequence similarity. When identifying relationships of this nature, the ability to find local regions of optimal similarity is advantageous over global alignments that optimize the overall alignment of two entire sequences. The paper describes a new method for genome sequence comparison. This algorithm can be used in a genomes data mining system. It provides a good theoretical improvement in accuracy with a modest sacrifice in speed as compared to the most commonly used alternatives. The method is based on the popular progressive approach, the dot plot method, but avoids the most serious pitfalls caused by the greedy nature of this technique. The new approach pre-processes a data set of all pair-wise alignments between the sequences. This provides a library of alignment information that can be used to guide the comparison. The algorithm is based on the similar segment method, i.e. having n similar identities in window of size L. The paper presents some results about the termination and correctness of the algorithm and how to include this algorithm into other comparison algorithms. The paper introduces the mechanism to create random sequences. These data will be our main benchmarks for comparing our algorithms. [Copyright &y& Elsevier]

Abstract: A properly engineered biomaterial for dental/orthopaedic applications must induce specific responses from the osteoblasts at the implant site. A most desirable response is an efficient adhesion, as it represents the first phase in the cell/material interaction and the quality of this phase will influence the cell''s capacity to organize into a new functional tissue. The four osteoblast-adhesive peptides discussed in this paper are mapped on the 339–364 sequence (339MAPRPSLAKKQRFRHRNRKGYRSQRG364) located in the primary heparin-binding site of human vitronectin (HVP). Adsorbed on a polystyrene scaffold, these peptides display different adhesive activities towards osteoblasts. In this paper we report on the structural analysis in solution of the peptides through NMR and computational techniques. We find that the peptides with the highest adhesive activities display a hydrophobic patch opposite to the charged surface candidate to interact with heparin. These findings suggest that the peptides might adsorb on the polystyrene support in a favourable orientation for their activity. Furthermore, molecular models obtained for the four peptides in solution were used in rigid docking simulations with a heparin model. Assuming that the peptide solution conformations are not very different from the polystyrene-adsorbed structures, the simulations reveal that peptide adhesive activity is also affected by the number of ionic interactions and spacing between charged residues. [Copyright &y& Elsevier]

Telomere homeostasis, a process that is essential for continued cell proliferation and genomic stability, is regulated by endogenous telomerase and a collection of associated proteins. In this paper, a protein called KIP (previously reported as a protein that binds specifically to DNA-dependent protein kinase), has been identified as a telomerase-regulating activity based on the following pieces of evidence. First, complexes between KIP and the catalytic subunit of telomerase (hTERT) were identified using the yeast two-hybrid technique. Second, antibodies specific to KIP immunoprecipitate human telomerase in cell-free extracts. Third, immunolocalization experiments demonstrate that KIP is a nuclear protein that co-localizes with hTERT in cells. Fourth, KIP binds to hTERT both in vitro and in vivo in the absence of human telomerase RNA or telomeric DNA, thus defining the catalytic subunit of telomerase as the site of physical interaction. Fifth, co-immunoprecipitation experiments suggest that KIP-hTERT complexes form readily in cells and that overexpression of KIP in telomerase-positive cells increases endogenous telomerase activity. Finally, continued overexpression of KIP (60 population doublings) resulted in cells with elongated telomeres; thus, KIP directly or indirectly stimulates telomerase activity through hTERT and contributes to telomere lengthening. The collective data in this paper suggest that KIP plays a positive role in telomere length maintenance and/or regulation and may represent a novel target for anti-cancer drug development. [ABSTRACT FROM AUTHOR]

As functional materials, chitin and chitosan offer a unique set of characteristics: biocompatibility, biodegradability to harmless products, nontoxicity, physiological inertness, antibacterial properties, heavy metal ions chelation, gel forming properties and hydrophilicity, and remarkable affinity to proteins. Owing to these characteristics, chitin- and chitosan-based materials, as yet underutilized, are predicted to be widely exploited in the near future especially in environmentally benign applications in systems working in biological environments, among others as enzyme immobilization supports. This paper is a review of the literature on enzymes immobilized on chitin- and chitosan-based materials, covering the last decade. One hundred fifty-eight papers on 63 immobilized enzymes for multiplicity of applications ranging from wine, sugar and fish industry, through organic compounds removal from wastewaters to sophisticated biosensors for both in situ measurements of environmental pollutants and metabolite control in artificial organs, are reviewed. [Copyright &y& Elsevier]

The IUPS Physiome Project is an internationally collaborative open-source project to provide a public domain framework for computational physiology, including the development of modelling standards, computational tools and web-accessible databases of models of structure and function at all spatial scales. A number of papers in this volume deal with the development of specific mathematical models of physiological processes. This paper stands back from the detail of individual models and reviews the current state of the IUPS Physiome Project including organ and organ system continuum models, the interpretation of constitutive law parameters in terms of micro-structural models, and markup languages for standardizing cellular processes. Some current practical applications of the physiome models are given and some of the challenges for the next 5 years of the Physiome Project at the level of organs, cells and proteins are proposed. [Copyright &y& Elsevier]

The introduction of novel proteins into foods carries a risk of eliciting allergic reactions in individuals sensitive to the introduced protein. Therefore, decision trees for evaluation of the risk have been developed, the latest being proposed by WHO/FAO early in 2001. Proteins developed using modern biotechnology and derived from fish are being considered for use in food and other applications, and since allergy to fish is well established, a potential risk from such proteins to susceptible human beings exists. The overall aim of the study was to investigate the potential allergenicity of an Ice Structuring Protein (ISP) originating from an arctic fish (the ocean pout, Macrozoarces americanus) using the newly developed decision tree proposed by FAO/WHO. The methods used were those proposed by FAO/WHO including amino acid sequence analysis for sequence similarity to known allergens, methods for assessing degradability under standardised conditions, assays for detection of specific IgE against the protein (Maxisorb RAST) and histamine release from human basophils. In the present paper we describe the serum screening phase of the study and discuss the overall application of the decision tree to the assessment of the potential allergenicity of ISP Type III. In an accompanying paper [Food Chem. Toxicol. 40 (2002) 965], we detail the specific methodology used for the sequence analysis and assessment of resistance to pepsin-catalysed proteolysis of this protein. The ISP showed no sequence similarity to known allergens nor was it stable to proteolytic degradation using standardised methods. Using sera from 20 patients with a well-documented clinical history of fish allergy, positive in skin prick tests to ocean pout, eel pout and eel were used, positive IgE-binding in vitro to extracts of the same fish was confirmed. The sera also elicited histamine release in vitro in the presence of the same extracts. The ISP was negative in all cases in the same experiments. Using the proposed decision tree, we demonstrated the safety of the ISP to patients already sensitised to fish, as well as to individuals potentially susceptible to producing IgE responses to proteins. Furthermore, the practicability of the new decision tree was confirmed. [Copyright &y& Elsevier]

Manganese dioxide (MnO 2) is a Mn deposit widely accumulated in the corrosion layer of pipelines, and iodide (I−) is a halogen ion frequently detected in waters. The biofilm dwelling on the corrosion scales often secretes extracellular polymeric substances (EPS) into drinking water. The paper aimed to study the I− oxidation by MnO 2 and iodinated disinfection byproducts (I-DBPs) formation with biofilm EPS as a precursor. More than 93% of formed free iodine was finally converted into organic iodine in the MnO 2 /I−/EPS system. Compared with humic acid, EPS had a lower carbonaceous I-DBPs (C-IDBPs) formation while a higher nitrogenous I-DBPs (N-IDBPs) formation. The formation of iodomethanes (I-THMs), iodoacetonitriles (I-HANs) and iodoacetic acids (I-HAAs) decreased with the increase of pH due to the weakening of polarization effect and redox potential, while the iodoacetamides (I-HAcAms) formation achieved the maximum at pH 6.0 due to the difference between the hydrolysis rate of I-HANs and decomposition rate of I-HAcAms. The I-DBPs formation was positively correlated with I− concentration, while negatively correlated with MnO 2 dose. Protein components displayed a higher formation of N-IDBPs and C-IDBPs than polysaccharide components due to higher nitrogen proportion and more iodination sites. Among 20 protein monomers, aspartic acid was considered as the most important precursor of the four investigated I-DBPs species. The paper is helpful to understand the I-DBPs formation when I− in the bulk water come into contact with Mn deposits attached by biofilm. [Display omitted] • EPS presented a higher FP of N-IDBPs but a lower FP of C-IDBPs than HA. • pH, I− concentration and MnO 2 dose showed a serious effect on I-DBPs yield. • The FP of I-DBPs from proteins was much higher than that from polysaccharides. • Among 20 amino acids in EPS proteins, Asp was the most important precursor. [ABSTRACT FROM AUTHOR]

Currently, synthetic polymers are extensively used due to their superior properties such as inexpensive and ease of processing. They are non-degradable and create pollution in the environment. There is a growing demand for the use of biodegradable polymers due to increasing atmospheric pollution. Excessive use of non-biodegradable polymers causes atmospheric pollution. Therefore many scientists suggested using polymers more and more ecologically. Therefore, soy Protein Isolate (SPI) is mostly used due to low cost and readily available material. It contains 90% protein with excellent biocompatibility, biodegradability and processibility properties. Synthetic polymers based materials are used in plastic packaging being inexpensive. SPI is incorporated into the synthetic polymer to improve degradation behavior of the product and reduces atmospheric pollution. It increases the viscosity of polymeric materials and becomes a gel or viscous when heated. The purpose of this review is to focus on the study of SPI based composites and nanocomposites. The inclusion of various organic and inorganic fillers in the macro, micro and nano scale in SPI based products have exceptional degradation properties. SPI based composite and nanocomposites found their applications in various fields such as food, agriculture, biotechnology, biodegradable foams and packaging of edible or non-edible materials. It is used in wood and paper industries as a replacement for synthetic materials as adhesives and coating materials. It is also utilized as a wound dressing application due to its excellent absorbing behavior. • This review paper focused on following: • Soy protein isolate polysaccharides based composites and nanocomposites. • Soy protein isolate based products have excellent biodegradability. • Soy protein isolate mostly used in packaging applications. [ABSTRACT FROM AUTHOR]

Cellulose has a long history dating back to ancient times in the evolution of humanity. It was a key material for basic needs, especially for the construction of shelters, paper making, which allowed our ancestors to perpetuate the valuable literary, philosophical or artistic works. In modern era, cellulose has acquired new dimensions of knowledge and scientific interest. This increased interest in cellulose is due to the need to exploit the still unknown resources that cellulose provides us, possibly due to the remarkable progress made lately in the field of fine characterization of the structure using sophisticated electron microscopes and other characterization techniques that have recently emerged. The growing demands of modern society in the direction of computerization and technology, have led the general interest to move from the classical writing paper to other types of "papers" that incorporates a high degree of ingenuity and intelligence, the so-called special papers, ranging from sensors, chips, motherboards, papers with a high degree of security, and many others. Among these, paper-based biosensors are of special interest, due to their high selectivity, simplicity, low price, and fast response. In this article we will review the new trends in the immobilization of biomolecules on various cellulose-based supports. In the first part, we will discuss the stages prior to the manufacture of a such support by specific chemical modification of the cellulosic substrate, followed by an overview of the most studied proteins, but also the most commonly used methods in monitoring protein adsorption on cellulosic substrates. • Cellulose modified surfaces for biomolecules attachment. • Adsorption of proteins on cellulose-based supports. • Different strategies to adsorb enzymes onto cellulosic supports. • Methods for the protein's adsorption monitoring. [ABSTRACT FROM AUTHOR]

In the companion paper, a whole-body, mechanistic model of protein turnover in a rodent was described and evaluated with independent data sets that used the flooding dose method. On the basis of fitted fluxes, the model was able to predict specific radioactivity changes in the protein and free leucine pools and whole-body protein fractional synthesis rate (FSR). In this paper, results of model simulations of specific radioactivity changes in the flooding dose, pulse dose and continuous infusion methods were compared and the influence of recycling, channeling and multiple protein pools on model behavior were analyzed. For all methods, the percentage of channeling must be estimated to determine whether the extracellular or intracellular pool specific radioactivities better approximate the aminoacyl tRNA pool specific radioactivity. Recycling also affects the specific radioactivity of the aminoacyl-tRNA pool and therefore must be estimated. An analysis of fits of the flooding dose data indicated that 100% channeling was occurring, but the percentage of recycling could not be determined. Multiple protein pools turning over at different rates overestimated FSR by 2-3% at early time points (5 min) and underestimated FSR by 3-6% at 60 min in the flooding dose method. For the pulse dose method, FSR was underestimated by 40-50% at 5 min and underestimated by 9-10% at 60 min. An increase in time to measure FSR caused a decrease in the estimate of FSR (18% over 3 h) for the flooding dose method and an increase in the estimate of FSR (144% over 3 h) for the pulse dose method. [ABSTRACT FROM AUTHOR]

One of the most important interactions responsible for protein folding and stability are hydrogen bonds between peptide groups. There is a constant competition between the water molecules and peptide groups in a hydrogen bond formation. Also side-chains take part in this process by reducing hydration of peptide group (shielding effect) that promotes the protein folding. In this paper, a new approach to take into account a shielding effect is presented. A modification of the energy function is derived and incorporated into the UNited RESidue (UNRES) force field. Canonical Molecular Dynamics and Replica Exchange Molecular Dynamics with UNRES force field is applied to study the influence of this effect on protein structure, folding kinetics and free energy landscapes. The results of test calculations suggest that even small contribution of this effect into energy function changes force field behavior as well as speeds up the folding process significantly. [ABSTRACT FROM AUTHOR]

The Golgi Apparatus (GA) is a key organelle for protein synthesis within the eukaryotic cell. The main task of GA is to modify and sort proteins for transport throughout the cell. Proteins permeate through the GA on the ER (Endoplasmic Reticulum) facing side (cis side) and depart on the other side (trans side). Based on this phenomenon, we get two types of GA proteins, namely, cis-Golgi protein and trans-Golgi protein. Any dysfunction of GA proteins can result in congenital glycosylation disorders and some other forms of difficulties that may lead to neurodegenerative and inherited diseases like diabetes, cancer and cystic fibrosis. So, the exact classification of GA proteins may contribute to drug development which will further help in medication. In this paper, we focus on building a new computational model that not only introduces easy ways to extract features from protein sequences but also optimizes classification of trans-Golgi and cis-Golgi proteins. After feature extraction, we have employed Random Forest (RF) model to rank the features based on the importance score obtained from it. After selecting the top ranked features, we have applied Support Vector Machine (SVM) to classify the sub-Golgi proteins. We have trained regression model as well as classification model and found the former to be superior. The model shows improved performance over all previous methods. As the benchmark dataset is significantly imbalanced, we have applied Synthetic Minority Over-sampling Technique (SMOTE) to the dataset to make it balanced and have conducted experiments on both versions. Our method, namely, identification of sub-Golgi Protein Types (isGPT), achieves accuracy values of 95.4%, 95.9% and 95.3% for 10-fold cross-validation test, jackknife test and independent test respectively. According to different performance metrics, isGPT performs better than state-of-the-art techniques. The source code of isGPT, along with relevant dataset and detailed experimental results, can be found at https://github.com/srautonu/isGPT. [ABSTRACT FROM AUTHOR]

This paper presents a new characterization method and a multistep kinetic mechanism for describing the pyrolysis process of algae fuels. Since third generation biomasses are still largely unexplored, we first organized a database by collecting literature information on the nature and main features of algal biomass. The algal species, both macro- and micro-algae, are constituted by proteins, carbohydrates and lipids, present in various amounts depending on the taxonomy and growing conditions. Noteworthy, algae contain higher levels of proteins, lipids, nitrogen and ashes compared to vegetal biomasses. Starting from the ultimate analysis and ash content, the biochemical composition of each algal species is defined in terms of proteins, carbohydrates, and lipids. To this aim, a limited number of representative reference species is first defined, based on atomic mass balances. The predicted biochemical compositions fairly agree with experimental information. Then, a multi-step semi-detailed kinetic mechanism of algae pyrolysis has been developed for the different reference components, following the same approach successfully applied for lignocellulosic biomasses. Moreover, a further release of ammonium, nitrates, and carbonates groups is estimated and related to the ash content. Despite the reduced number of reference species and the rough assumptions to reduce the complexity of the overall problem, the model is already able to satisfactorily predict the pyrolysis behavior of micro- and macro-algae. To our knowledge, and despite all the strong simplifications, this is the first method to characterize algae species, as well as the first kinetic model able to predict the algae pyrolysis process. [ABSTRACT FROM AUTHOR]

We used the Langmuir technique to investigate the binding of the bovine α-lactalbumin (BLA III) to the oleic acid (OA) monolayer in gastric conditions (pH 2.0 and 36.6 °C). Both substances are components of the BAMLET complex, which is beneficial to human health. The monolayer studies have been completed with BAM imaging and PM-IRRAS spectra. This paper explores the interfacial behavior of the lipid monolayer in the presence of the protein. It proves that the higher the concentration of protein in the subphase, the higher the increase in the relative surface pressure of the OA monolayer is, until the additional amount of protein affects the maximmum film response. We also discussed the MIP (maximum insertion pressure) value and analyzed the infrared spectra to prove that BLA III interacts with OA at the interface. We focused on the kinetics of the interaction between these components. We noticed that after protein adsorption at the interface (which rate depends on BLA III concentration), the protein penetrates the lipid monolayer, followed by film rearrangement (the protein forces on fatty acid molecules to change their orientation) until finally a stable lipid-protein complex is formed at the air-water interface. This multi-stage process is relevant to the course of a relaxation curve, which demonstrates the monolayer response on protein injection. This paper explores the physicochemical phenomena which fully recognized may open the door to numerous applications of these lipid-protein system. Unlabelled Image • The oleic acid and α-lactalbumin form the interfacial complex at pH 2.0 and 36.6 °C • In the gastric condition, protein penetrates the oleic acid monolayer • The protein molecules induce film rearrangement • Tightly packed monolayer limits the ability of the protein to penetrate the film • The number of protein molecules penetrating the film is finite under given condition [ABSTRACT FROM AUTHOR]